Enhanced analysis of a Peace Corp worker with CFS from a jungle infection

Reader Notes

“My official diagnosis is ME/CFS from Stanford and I’ve tried a lot of different treatments including a year of Valcyte. I’ve gotten everything under the sun tested. Have such a high amount of Candida that a Gastro Doc said that I must have an autoimmune disease but found nothing.”

This all started when I was a Peace Corps Worker in Panama. I got really sick in the jungle where I was working and after one day in the river I started getting a tingling feeling in my out extremities. It then turned to burning sensation, fatigue, brain fog, restless legs, unable to sleep, tiredness, unrestful sleep, and IBS. Its been 5 years and I’ve a lot of treatments.

Standard Items:

  • Lactobacillus: 0.01x
  • Bifidobacterium: 0.88x
  • Akkermansia:  1.06x
  • Diversity:  79%ile
  • Firmicutes to Bacteroidetes: 1.4:1 (Normal 2.1:1)

Uncommon Bacteria

Bacteria name Rank % of Samples
Defluviitaleaceae Family 0.4%
Caldicoprobacter Genus 3.1%
Parasporobacterium Genus 3.5%

High Bacteria

Paraprevotella: 4.37 X
Parabacteroides:  3.87 X
Moryella: 2.56 X
Peptococcus: 2.09 X
Terrisporobacter: 1.96 X
Thalassospira: 1.90 X
Odoribacter: 1.52 X


Bottom Line Suggestions

The lists below are done by merging the lists from the deep dives linked above. Some items may encourage one genus and discourage another genus — those are removed (unless it seems that it strongly predominates on one). The impact on Lactobacillus, Bifidobacterium and E.Coli are intentionally ignored [See this post for the logic]. This is all based on applying logic to the results of studies — thus theoretical. This is an addition (not a replacement) to this overview post.


  • Amoxicillin-Clavulanate antibiotics
  • Canola Oil
  • Lactobacillus caseiLactobacillus paracasei
  • Lactobacillus rhamnosus
  • Lingonberries
  • Proton-pump inhibitors (PPI)
  • Resistant Starch
  • Rhubarb
  • Rice bran
  • Saccharomyces boulardii
  • Sleep Apnea
  • Walnuts


  • Berberine
  • Capsaicin(chili peppers)
  • Cinnamon
  • Cranberry
  • Flaxseed
  • Gallate (tea)
  • High Fat Diet
  • Lactobacillus reuteri
  • Metronidazole antibiotics
  • Palm kernel meal


This microbiome had many genus uncommon with CFS. Given that the onset was probably a tropical infection, and each infection alters the microbiome in distinctive manners, I suspect this was a contributory factor for the unusual genus appearing as well as  Bifidobacterium and Akkermansia being close to normal. In terms of general supplements from this post, these are likely the most important

To the above, dairy should be added to increase the Firmicutes to Bacteroidetes ratio (see this post)

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.